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The understanding of the dynamic of soil-borne diseases is related to the microbial composition of the rhizosphere which is the key to progress in the field of biological control.  Trichoderma  spp. is commonly used as a biological control agent. The use of next generation sequencing approaches and quantitative PCR are two successful approaches to assess the effect of using compost as substrate fortified with two  Trichoderma  strains ( Trichoderma harzianum  or  Trichoderma asperellum ) on bacterial and fungal communities in pepper rhizosphere infected with  Phytophthora nicotianae . The results showed changes in the bacterial rhizosphere community not attributed to the  Trichoderma  strain, but to the pathogen infection, while, fungi were not affected by pathogen infection and depended on the type of substrate. The  Trichoderma asperellum  fortified compost was the most effective combination against the pathogen. This could indicate that the effect of fortified composts is greater than compost itself and the biocontrol effect should be attributed to the  Trichoderma  strains rather than the compost microbiota, although some microorganisms could help with the biocontrol effect.

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae